Most plant traits of agronomic importance are polygenic, otherwise known as quantitative, traits. A quantitative trait is controlled by several genes located at various locations, or loci, in the plant's genome. The multiple genes have a cumulative effect which contributes to the continuous range of phenotypes observed in many plant traits. These genes are referred to as quantitative trait loci (“QTL”).
Multiple experimental paradigms have been developed to identify and analyze QTL. In general, these paradigms involve crossing one or more parental pairs, which can be, for example, a single pair derived from two inbred strains, or multiple related or unrelated parents of different inbred strains or lines, which each exhibit different characteristics relative to the phenotypic trait of interest. The parents and a population of progeny are genotyped, typically for multiple marker loci, and evaluated for the trait of interest. QTL associated with traits of interest are identified based on the significant statistical correlations between the marker genotype(s) and the traits of interest phenotype of the evaluated progeny plants. Numerous methods for determining whether markers are genetically linked to a QTL (or to another marker) are known to those of skill in the art and include, e.g., interval mapping (Lander and Botstein, “Mapping Mendelian Factors Underlying Quantitative Traits Using RFLP Linkage Maps,” Genetics 121:185-99 (1989)), regression mapping (Haley and Knott “A Simple Regression Method for Mapping Quantitative Trait Loci In Line Crosses Using Flanking Markers,” Heredity 69:315-324 (1992)) or MQM mapping (Jansen, “Controlling the Type I and Type II Errors in Mapping Quantitative Trait Loci” Genetics 138:871-881 (1994)).
Measurable traits related to ear productivity in maize include kernel row number (“KRN”), kernel count (“KC”), kernel weight (“KW”), average kernel weight (“AKW”), cob weight (“CW”), cob length (“CL”), cob diameter (“CD”), and seedling dry weight (“SDW”). These traits are considered quantitative traits and can be studied via QTL mapping. With this approach, genomic regions regulating a measurable trait are identified in populations segregating for the trait. See, e.g., Veldboom et al., “Molecular Marker-facilitated Studies In an Elite Maize Population: 1. Linkage Analysis and Determination of QTL for Morphological Traits,” Theor. Appl. Genet. 88(1):7-16 (1994); Beavis et al., “Identification of Quantitative Trait Loci Using a Small Sample of Toperossed and F4 Progeny from Maize,” Crop Sci. 34:882-896 (1994); Austin et al., “Comparative Mapping in F-2:3 and F-6:7 Generations of Quantitative Trait Loci for Grain Yield and Yield Components In Maize,” Theor. Appl. Genet. 92(7):817-826 (1996); Veldboom et al., “Genetic Mapping of Quantitative Trait Loci in Maize in Stress and Nonstress Environments. 1. Grain Yield and Yield Components,” Crop Sci. 36(5):1310-1319 (1996); Veldboom et al., “Genetic Mapping of Quantitative Trait Loci in Maize in Stress and Nonstress Environments. 2. Plant Height and Flowering,” Crop Sci. 36(5):1320-1327 (1996); Bommert et al., “Thick Tassel Dwarf1 Encodes a Putative Maize Ortholog of the Arabidopsis CLAVATA1 Leucine-rich Repeat Receptor-like Kinase,” Development 132(6):1235-45 (2005); Tang et al., “Dissection of the Genetic Basis of Heterosis in an Elite Maize Hybrid by QTL Mapping In an Immortalized F2 Population,” Theor. Appl. Genet. 120(2):333-40 (2009).
A primary motivation for development of molecular markers in crop species is the potential for increased efficiency in plant breeding through marker assisted selection (“MAS”). Genetic marker alleles, or alternatively, identified QTL alleles, are used to identify plants that contain a desired genotype at one or more loci, and that are expected to transfer the desired genotype, along with a desired phenotype, to their progeny. Genetic marker alleles (or QTL alleles) can be used to identify plants that contain a desired genotype at one locus, or at several unlinked or linked loci (e.g., a haplotype), and that would be expected to transfer the desired genotype, along with a desired phenotype to their progeny.
Breeding, e.g., for increased ear productivity in maize via the traditional approach is difficult due to the multigenic nature of these traits. What is needed in the art is a means to identify genes conferring increased ear productivity using molecular markers. These markers can then be (i) used to tag the favorable alleles of these genes in segregating maize populations and (ii) employed to make selection for increased ear productivity more effective.
The present invention is directed to achieving these and other objectives and to overcoming limitations in the art.